Projects

SED-ML Meeting

The Simulation Experiment Description Markup Language (SED-ML) is an exchange format for simulation experiments in computational biology and related fields.

The first version of the language has been released as SED-ML L1V1 in March 2011. The further development and promotion of SED-ML is one of the project goals of the BMBF-funded SEMS project at the SBI.

The first workshop of the SEMS project aims to evaluate the current status of SED-ML, in particular with respect to:

How is SED-ML currently being used by other projects? Which concepts of SED-ML are of most interest to other research groups implementing SED-ML support?

What are the applications of SED-ML in systems biology, medicine and the neuro sciences?

Which software tools support SED-ML? Which databases offer links to SED-ML descriptions?

We aim close the meeting with an outlook for the year 2013, collecting to-dos for further development of SED-ML.

Schedule

The meeting will take place from the 19th-22nd of November 2012 at the Department of Systems Biology and Bioinformatics at the University of Rostock (directions).

MON, 19th of November 2012

12:00 – 13:00

Arrival/self-funded lunch (Mensa)

13:30 – 15:00

Invited Talk: COPASI (Sven Sahle, BIOQUANT)

15:00 – 15:30

Coffee break

15:30 – 17:00

Session I : Plan for days 2 + 3, Nested vote

19:30 Uhr

Workshop dinner: Warmbad

TUE, 20th of November 2012

8:45- 9:00

Welcome & Coffee

09:00 -10:00

Session II: Editors meeting

10:00- 11:30

Session III: Nested / multiple sub-tasks

11:30 – 13:00

Self-funded lunch

13:00 – 14:00

Session IV: Nested/multiple sub-tasks

14:00 – 15:30

Session V: Parameter estimation

15:00 – 15:30

Coffee break

15:30 – 17:00

Session VI: Parameter estimation/post-processing

WED, 21st of November 2012

8:45 - 9:00

Welcome & Coffee

09:00 -11:00

Session VII: SED-ML specification update

11:00 – 12:30

Self-funded lunch (Mensa)

12:30- 14:30

Session VIII: Discussion further development

14:30 – 15:00

Coffee break

15:00 – 17:00

Session IX: Discussion further development

17:00

Workshop summary

Useful information

ParticipationYou are welcome to join the meeting either in person of remotely through Evo.

Remote attendanceIf you wish to attend remotely, please connect to the Evo meeting via Evo gate. We will unfortunately not be able to broadcast the talk by Sven Sahle on Monday, but will be online from 3:00pm.